0.026645
0.000000
0.000000
0.000000
0.026645
0.000000
0.000000
0.000000
0.009929
0.00000
0.00000
0.00000
Kirby, K.A.
Sarafianos, S.G.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.00
90.00
37.530
37.530
100.720
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-peptide linking
H2 O
18.015
WATER
non-polymer
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C5 H11 N O2 S
149.211
y
METHIONINE
L-peptide linking
Mg 2
24.305
MAGNESIUM ION
non-polymer
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
L-peptide linking
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
N
1
N
N
N
2
S
C
N
3
N
C
N
4
N
O
N
5
N
C
N
6
N
O
N
7
N
H
N
8
N
H
N
9
N
H
N
10
N
H
N
11
N
H
N
12
N
H
N
13
N
H
N
14
N
N
N
15
S
C
N
16
N
C
N
17
N
O
N
18
N
C
N
19
N
C
N
20
N
C
N
21
N
N
N
22
N
C
N
23
N
N
N
24
N
N
N
25
N
O
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
H
N
31
N
H
N
32
N
H
N
33
N
H
N
34
N
H
N
35
N
H
N
36
N
H
N
37
N
H
N
38
N
H
N
39
N
H
N
40
N
H
N
41
N
N
N
42
S
C
N
43
N
C
N
44
N
O
N
45
N
C
N
46
N
C
N
47
N
O
N
48
N
N
N
49
N
O
N
50
N
H
N
51
N
H
N
52
N
H
N
53
N
H
N
54
N
H
N
55
N
H
N
56
N
H
N
57
N
H
N
58
N
N
N
59
S
C
N
60
N
C
N
61
N
O
N
62
N
C
N
63
N
C
N
64
N
O
N
65
N
O
N
66
N
O
N
67
N
H
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
H
N
72
N
H
N
73
N
H
N
74
N
N
N
75
R
C
N
76
N
C
N
77
N
O
N
78
N
C
N
79
N
S
N
80
N
O
N
81
N
H
N
82
N
H
N
83
N
H
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
N
N
89
S
C
N
90
N
C
N
91
N
O
N
92
N
C
N
93
N
C
N
94
N
C
N
95
N
O
N
96
N
N
N
97
N
O
N
98
N
H
N
99
N
H
N
100
N
H
N
101
N
H
N
102
N
H
N
103
N
H
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
H
N
108
N
N
N
109
S
C
N
110
N
C
N
111
N
O
N
112
N
C
N
113
N
C
N
114
N
C
N
115
N
O
N
116
N
O
N
117
N
O
N
118
N
H
N
119
N
H
N
120
N
H
N
121
N
H
N
122
N
H
N
123
N
H
N
124
N
H
N
125
N
H
N
126
N
H
N
127
N
N
N
128
N
C
N
129
N
C
N
130
N
O
N
131
N
O
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
N
N
138
S
C
N
139
N
C
N
140
N
O
N
141
N
C
Y
142
N
C
Y
143
N
N
Y
144
N
C
Y
145
N
C
Y
146
N
N
N
147
N
O
N
148
N
H
N
149
N
H
N
150
N
H
N
151
N
H
N
152
N
H
N
153
N
H
N
154
N
H
N
155
N
H
N
156
N
H
N
157
N
H
N
158
N
O
N
159
N
H
N
160
N
H
N
161
N
N
N
162
S
C
N
163
N
C
N
164
N
O
N
165
S
C
N
166
N
C
N
167
N
C
N
168
N
C
N
169
N
O
N
170
N
H
N
171
N
H
N
172
N
H
N
173
N
H
N
174
N
H
N
175
N
H
N
176
N
H
N
177
N
H
N
178
N
H
N
179
N
H
N
180
N
H
N
181
N
H
N
182
N
H
N
183
N
N
N
184
S
C
N
185
N
C
N
186
N
O
N
187
N
C
N
188
N
C
N
189
N
C
N
190
N
C
N
191
N
O
N
192
N
H
N
193
N
H
N
194
N
H
N
195
N
H
N
196
N
H
N
197
N
H
N
198
N
H
N
199
N
H
N
200
N
H
N
201
N
H
N
202
N
H
N
203
N
H
N
204
N
H
N
205
N
N
N
206
S
C
N
207
N
C
N
208
N
O
N
209
N
C
N
210
N
C
N
211
N
C
N
212
N
C
N
213
N
N
N
214
N
O
N
215
N
H
N
216
N
H
N
217
N
H
N
218
N
H
N
219
N
H
N
220
N
H
N
221
N
H
N
222
N
H
N
223
N
H
N
224
N
H
N
225
N
H
N
226
N
H
N
227
N
H
N
228
N
H
N
229
N
H
N
230
N
N
N
231
S
C
N
232
N
C
N
233
N
O
N
234
N
C
N
235
N
C
N
236
N
S
N
237
N
C
N
238
N
O
N
239
N
H
N
240
N
H
N
241
N
H
N
242
N
H
N
243
N
H
N
244
N
H
N
245
N
H
N
246
N
H
N
247
N
H
N
248
N
H
N
249
N
H
N
250
N
MG
N
251
N
N
N
252
S
C
N
253
N
C
N
254
N
O
N
255
N
C
Y
256
N
C
Y
257
N
C
Y
258
N
C
Y
259
N
C
Y
260
N
C
Y
261
N
C
N
262
N
O
N
263
N
H
N
264
N
H
N
265
N
H
N
266
N
H
N
267
N
H
N
268
N
H
N
269
N
H
N
270
N
H
N
271
N
H
N
272
N
H
N
273
N
H
N
274
N
N
N
275
S
C
N
276
N
C
N
277
N
O
N
278
N
C
N
279
N
C
N
280
N
C
N
281
N
O
N
282
N
H
N
283
N
H
N
284
N
H
N
285
N
H
N
286
N
H
N
287
N
H
N
288
N
H
N
289
N
H
N
290
N
H
N
291
N
N
N
292
S
C
N
293
N
C
N
294
N
O
N
295
N
C
N
296
N
O
N
297
N
O
N
298
N
H
N
299
N
H
N
300
N
H
N
301
N
H
N
302
N
H
N
303
N
H
N
304
N
H
N
305
N
N
N
306
S
C
N
307
N
C
N
308
N
O
N
309
R
C
N
310
N
O
N
311
N
C
N
312
N
O
N
313
N
H
N
314
N
H
N
315
N
H
N
316
N
H
N
317
N
H
N
318
N
H
N
319
N
H
N
320
N
H
N
321
N
H
N
322
N
N
N
323
S
C
N
324
N
C
N
325
N
O
N
326
N
C
Y
327
N
C
Y
328
N
C
Y
329
N
C
Y
330
N
N
Y
331
N
C
Y
332
N
C
Y
333
N
C
Y
334
N
C
Y
335
N
C
N
336
N
O
N
337
N
H
N
338
N
H
N
339
N
H
N
340
N
H
N
341
N
H
N
342
N
H
N
343
N
H
N
344
N
H
N
345
N
H
N
346
N
H
N
347
N
H
N
348
N
H
N
349
N
N
N
350
S
C
N
351
N
C
N
352
N
O
N
353
N
C
Y
354
N
C
Y
355
N
C
Y
356
N
C
Y
357
N
C
Y
358
N
C
Y
359
N
C
N
360
N
O
N
361
N
O
N
362
N
H
N
363
N
H
N
364
N
H
N
365
N
H
N
366
N
H
N
367
N
H
N
368
N
H
N
369
N
H
N
370
N
H
N
371
N
H
N
372
N
H
N
373
N
N
N
374
S
C
N
375
N
C
N
376
N
O
N
377
N
C
N
378
N
C
N
379
N
C
N
380
N
O
N
381
N
H
N
382
N
H
N
383
N
H
N
384
N
H
N
385
N
H
N
386
N
H
N
387
N
H
N
388
N
H
N
389
N
H
N
390
N
H
N
391
N
H
N
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
doub
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
sing
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
doub
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
sing
N
25
N
sing
N
26
N
sing
N
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
doub
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
doub
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
doub
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
sing
N
57
N
sing
N
58
N
sing
N
59
N
sing
N
60
N
sing
N
61
N
doub
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
doub
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
doub
N
77
N
sing
N
78
N
sing
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
sing
N
84
N
sing
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
doub
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
sing
N
97
N
doub
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
doub
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
sing
N
115
N
sing
N
116
N
doub
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
doub
N
127
N
sing
N
128
N
sing
N
129
N
sing
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
doub
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
Y
140
N
sing
Y
141
N
doub
Y
142
N
doub
N
143
N
sing
Y
144
N
sing
N
145
N
sing
Y
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
sing
N
154
N
sing
N
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
doub
N
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
sing
N
164
N
sing
N
165
N
sing
N
166
N
sing
N
167
N
sing
N
168
N
sing
N
169
N
sing
N
170
N
sing
N
171
N
sing
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
doub
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
sing
N
188
N
sing
N
189
N
sing
N
190
N
sing
N
191
N
sing
N
192
N
sing
N
193
N
sing
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
sing
N
198
N
sing
N
199
N
sing
N
200
N
doub
N
201
N
sing
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
sing
N
206
N
sing
N
207
N
sing
N
208
N
sing
N
209
N
sing
N
210
N
sing
N
211
N
sing
N
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
sing
N
219
N
sing
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
doub
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
sing
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
sing
N
235
N
sing
N
236
N
sing
N
237
N
sing
N
238
N
sing
N
239
N
sing
N
240
N
sing
N
241
N
sing
N
242
N
sing
N
243
N
doub
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
Y
248
N
doub
Y
249
N
sing
Y
250
N
sing
N
251
N
sing
Y
252
N
doub
N
253
N
sing
Y
254
N
doub
N
255
N
sing
Y
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
sing
N
262
N
sing
N
263
N
sing
N
264
N
sing
N
265
N
sing
N
266
N
doub
N
267
N
sing
N
268
N
sing
N
269
N
sing
N
270
N
sing
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
sing
N
275
N
sing
N
276
N
sing
N
277
N
sing
N
278
N
sing
N
279
N
sing
N
280
N
sing
N
281
N
sing
N
282
N
sing
N
283
N
doub
N
284
N
sing
N
285
N
sing
N
286
N
sing
N
287
N
sing
N
288
N
sing
N
289
N
sing
N
290
N
sing
N
291
N
sing
N
292
N
sing
N
293
N
sing
N
294
N
sing
N
295
N
sing
N
296
N
doub
N
297
N
sing
N
298
N
sing
N
299
N
sing
N
300
N
sing
N
301
N
sing
N
302
N
sing
N
303
N
sing
N
304
N
sing
N
305
N
sing
N
306
N
sing
N
307
N
sing
N
308
N
sing
N
309
N
sing
N
310
N
sing
N
311
N
sing
N
312
N
doub
N
313
N
sing
N
314
N
sing
N
315
N
sing
N
316
N
sing
Y
317
N
doub
Y
318
N
sing
Y
319
N
sing
N
320
N
sing
Y
321
N
doub
Y
322
N
sing
Y
323
N
sing
N
324
N
sing
Y
325
N
sing
Y
326
N
doub
N
327
N
sing
Y
328
N
doub
N
329
N
sing
Y
330
N
sing
N
331
N
sing
N
332
N
sing
N
333
N
sing
N
334
N
sing
N
335
N
sing
N
336
N
sing
N
337
N
sing
N
338
N
sing
N
339
N
sing
N
340
N
doub
N
341
N
sing
N
342
N
sing
N
343
N
sing
N
344
N
sing
Y
345
N
doub
Y
346
N
sing
Y
347
N
sing
N
348
N
sing
Y
349
N
doub
N
350
N
sing
Y
351
N
doub
N
352
N
sing
Y
353
N
sing
N
354
N
sing
N
355
N
sing
N
356
N
sing
N
357
N
sing
N
358
N
sing
N
359
N
sing
N
360
N
sing
N
361
N
sing
N
362
N
sing
N
363
N
sing
N
364
N
doub
N
365
N
sing
N
366
N
sing
N
367
N
sing
N
368
N
sing
N
369
N
sing
N
370
N
sing
N
371
N
sing
N
372
N
sing
N
373
N
sing
N
374
N
sing
N
375
N
sing
US
Antimicrob.Agents Chemother.
AMACCQ
0788
0066-4804
56
2048
2061
10.1128/AAC.06000-11
22252812
Structural and Inhibition Studies of the RNase H Function of Xenotropic Murine Leukemia Virus-Related Virus Reverse Transcriptase.
2012
10.2210/pdb3p1g/pdb
pdb_00003p1g
1
CCD
2010-09-24
NOIR-1
SINGLE WAVELENGTH
M
x-ray
1
1.0
1.0
4.2.2
ALS
1.0
SYNCHROTRON
ALS BEAMLINE 4.2.2
17968.305
Xenotropic Murine Leukemia Virus-Related Virus (XMRV) RNase H Domain
595-605 deletion mutant
1
man
polymer
24.305
MAGNESIUM ION
1
syn
non-polymer
18.015
water
162
nat
water
no
no
GSILAETHGTRPDLTDQPIPDADYTWYTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMAEG
KKLNVYTDSRYAFATAHVHSEGREIKNKNEILALLKALFLPKRLSIIHCPGHQKGNSAEARGNRMADQAAREAAMKAVLE
TSTLL
GSILAETHGTRPDLTDQPIPDADYTWYTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMAEG
KKLNVYTDSRYAFATAHVHSEGREIKNKNEILALLKALFLPKRLSIIHCPGHQKGNSAEARGNRMADQAAREAAMKAVLE
TSTLL
A
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
sample
438045
Xenotropic MuLV-related virus
562
Escherichia coli
1
1.97
37.68
VAPOR DIFFUSION, HANGING DROP
4.7
PEG 1500, Magnesium Chloride, Sodium Citrate, pH 4.7, Vapor Diffusion, Hanging Drop, temperature 291K
291
chem_comp_atom
chem_comp_bond
database_2
pdbx_struct_conn_angle
struct_conn
struct_ref_seq_dif
struct_site
repository
Initial release
Version format compliance
Database references
Database references
Data collection
Database references
Derived calculations
1
0
2010-10-13
1
1
2011-07-13
1
2
2012-02-01
1
3
2012-04-04
1
4
2024-02-21
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_struct_conn_angle.ptnr1_auth_comp_id
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_alt_id
_pdbx_struct_conn_angle.ptnr1_label_asym_id
_pdbx_struct_conn_angle.ptnr1_label_atom_id
_pdbx_struct_conn_angle.ptnr1_label_comp_id
_pdbx_struct_conn_angle.ptnr1_label_seq_id
_pdbx_struct_conn_angle.ptnr3_auth_comp_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_alt_id
_pdbx_struct_conn_angle.ptnr3_label_asym_id
_pdbx_struct_conn_angle.ptnr3_label_atom_id
_pdbx_struct_conn_angle.ptnr3_label_comp_id
_pdbx_struct_conn_angle.ptnr3_label_seq_id
_pdbx_struct_conn_angle.value
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
2010-09-30
REL
REL
MG
MAGNESIUM ION
HOH
water
MG
163
2
MG
MG
163
A
HOH
1
3
HOH
HOH
1
A
HOH
2
3
HOH
HOH
2
A
HOH
3
3
HOH
HOH
3
A
HOH
4
3
HOH
HOH
4
A
HOH
5
3
HOH
HOH
5
A
HOH
6
3
HOH
HOH
6
A
HOH
7
3
HOH
HOH
7
A
HOH
8
3
HOH
HOH
8
A
HOH
9
3
HOH
HOH
9
A
HOH
10
3
HOH
HOH
10
A
HOH
11
3
HOH
HOH
11
A
HOH
12
3
HOH
HOH
12
A
HOH
13
3
HOH
HOH
13
A
HOH
14
3
HOH
HOH
14
A
HOH
15
3
HOH
HOH
15
A
HOH
16
3
HOH
HOH
16
A
HOH
17
3
HOH
HOH
17
A
HOH
18
3
HOH
HOH
18
A
HOH
19
3
HOH
HOH
19
A
HOH
20
3
HOH
HOH
20
A
HOH
21
3
HOH
HOH
21
A
HOH
22
3
HOH
HOH
22
A
HOH
23
3
HOH
HOH
23
A
HOH
24
3
HOH
HOH
24
A
HOH
25
3
HOH
HOH
25
A
HOH
26
3
HOH
HOH
26
A
HOH
27
3
HOH
HOH
27
A
HOH
28
3
HOH
HOH
28
A
HOH
29
3
HOH
HOH
29
A
HOH
30
3
HOH
HOH
30
A
HOH
31
3
HOH
HOH
31
A
HOH
32
3
HOH
HOH
32
A
HOH
33
3
HOH
HOH
33
A
HOH
34
3
HOH
HOH
34
A
HOH
35
3
HOH
HOH
35
A
HOH
36
3
HOH
HOH
36
A
HOH
37
3
HOH
HOH
37
A
HOH
38
3
HOH
HOH
38
A
HOH
39
3
HOH
HOH
39
A
HOH
40
3
HOH
HOH
40
A
HOH
41
3
HOH
HOH
41
A
HOH
42
3
HOH
HOH
42
A
HOH
43
3
HOH
HOH
43
A
HOH
44
3
HOH
HOH
44
A
HOH
45
3
HOH
HOH
45
A
HOH
46
3
HOH
HOH
46
A
HOH
47
3
HOH
HOH
47
A
HOH
48
3
HOH
HOH
48
A
HOH
49
3
HOH
HOH
49
A
HOH
50
3
HOH
HOH
50
A
HOH
51
3
HOH
HOH
51
A
HOH
52
3
HOH
HOH
52
A
HOH
53
3
HOH
HOH
53
A
HOH
54
3
HOH
HOH
54
A
HOH
55
3
HOH
HOH
55
A
HOH
56
3
HOH
HOH
56
A
HOH
57
3
HOH
HOH
57
A
HOH
58
3
HOH
HOH
58
A
HOH
59
3
HOH
HOH
59
A
HOH
60
3
HOH
HOH
60
A
HOH
61
3
HOH
HOH
61
A
HOH
62
3
HOH
HOH
62
A
HOH
63
3
HOH
HOH
63
A
HOH
64
3
HOH
HOH
64
A
HOH
65
3
HOH
HOH
65
A
HOH
66
3
HOH
HOH
66
A
HOH
67
3
HOH
HOH
67
A
HOH
68
3
HOH
HOH
68
A
HOH
69
3
HOH
HOH
69
A
HOH
70
3
HOH
HOH
70
A
HOH
71
3
HOH
HOH
71
A
HOH
72
3
HOH
HOH
72
A
HOH
73
3
HOH
HOH
73
A
HOH
74
3
HOH
HOH
74
A
HOH
75
3
HOH
HOH
75
A
HOH
76
3
HOH
HOH
76
A
HOH
77
3
HOH
HOH
77
A
HOH
78
3
HOH
HOH
78
A
HOH
79
3
HOH
HOH
79
A
HOH
80
3
HOH
HOH
80
A
HOH
81
3
HOH
HOH
81
A
HOH
82
3
HOH
HOH
82
A
HOH
83
3
HOH
HOH
83
A
HOH
84
3
HOH
HOH
84
A
HOH
85
3
HOH
HOH
85
A
HOH
86
3
HOH
HOH
86
A
HOH
87
3
HOH
HOH
87
A
HOH
88
3
HOH
HOH
88
A
HOH
89
3
HOH
HOH
89
A
HOH
90
3
HOH
HOH
90
A
HOH
91
3
HOH
HOH
91
A
HOH
92
3
HOH
HOH
92
A
HOH
93
3
HOH
HOH
93
A
HOH
94
3
HOH
HOH
94
A
HOH
95
3
HOH
HOH
95
A
HOH
96
3
HOH
HOH
96
A
HOH
97
3
HOH
HOH
97
A
HOH
98
3
HOH
HOH
98
A
HOH
99
3
HOH
HOH
99
A
HOH
100
3
HOH
HOH
100
A
HOH
101
3
HOH
HOH
101
A
HOH
102
3
HOH
HOH
102
A
HOH
103
3
HOH
HOH
103
A
HOH
104
3
HOH
HOH
104
A
HOH
105
3
HOH
HOH
105
A
HOH
106
3
HOH
HOH
106
A
HOH
107
3
HOH
HOH
107
A
HOH
108
3
HOH
HOH
108
A
HOH
109
3
HOH
HOH
109
A
HOH
110
3
HOH
HOH
110
A
HOH
111
3
HOH
HOH
111
A
HOH
112
3
HOH
HOH
112
A
HOH
113
3
HOH
HOH
113
A
HOH
114
3
HOH
HOH
114
A
HOH
115
3
HOH
HOH
115
A
HOH
116
3
HOH
HOH
116
A
HOH
117
3
HOH
HOH
117
A
HOH
118
3
HOH
HOH
118
A
HOH
119
3
HOH
HOH
119
A
HOH
120
3
HOH
HOH
120
A
HOH
121
3
HOH
HOH
121
A
HOH
122
3
HOH
HOH
122
A
HOH
123
3
HOH
HOH
123
A
HOH
124
3
HOH
HOH
124
A
HOH
125
3
HOH
HOH
125
A
HOH
126
3
HOH
HOH
126
A
HOH
127
3
HOH
HOH
127
A
HOH
128
3
HOH
HOH
128
A
HOH
129
3
HOH
HOH
129
A
HOH
130
3
HOH
HOH
130
A
HOH
131
3
HOH
HOH
131
A
HOH
132
3
HOH
HOH
132
A
HOH
133
3
HOH
HOH
133
A
HOH
134
3
HOH
HOH
134
A
HOH
135
3
HOH
HOH
135
A
HOH
136
3
HOH
HOH
136
A
HOH
137
3
HOH
HOH
137
A
HOH
138
3
HOH
HOH
138
A
HOH
139
3
HOH
HOH
139
A
HOH
140
3
HOH
HOH
140
A
HOH
141
3
HOH
HOH
141
A
HOH
142
3
HOH
HOH
142
A
HOH
143
3
HOH
HOH
143
A
HOH
144
3
HOH
HOH
144
A
HOH
145
3
HOH
HOH
145
A
HOH
146
3
HOH
HOH
146
A
HOH
147
3
HOH
HOH
147
A
HOH
148
3
HOH
HOH
148
A
HOH
149
3
HOH
HOH
149
A
HOH
150
3
HOH
HOH
150
A
HOH
151
3
HOH
HOH
151
A
HOH
152
3
HOH
HOH
152
A
HOH
153
3
HOH
HOH
153
A
HOH
154
3
HOH
HOH
154
A
HOH
155
3
HOH
HOH
155
A
HOH
156
3
HOH
HOH
156
A
HOH
157
3
HOH
HOH
157
A
HOH
158
3
HOH
HOH
158
A
HOH
159
3
HOH
HOH
159
A
HOH
160
3
HOH
HOH
160
A
HOH
161
3
HOH
HOH
161
A
HOH
162
3
HOH
HOH
162
A
n
1
496
A
n
2
497
A
n
3
498
A
n
4
499
A
ALA
500
n
5
ALA
500
A
GLU
501
n
6
GLU
501
A
THR
502
n
7
THR
502
A
HIS
503
n
8
HIS
503
A
GLY
504
n
9
GLY
504
A
THR
505
n
10
THR
505
A
ARG
506
n
11
ARG
506
A
PRO
507
n
12
PRO
507
A
ASP
508
n
13
ASP
508
A
LEU
509
n
14
LEU
509
A
THR
510
n
15
THR
510
A
ASP
511
n
16
ASP
511
A
GLN
512
n
17
GLN
512
A
PRO
513
n
18
PRO
513
A
ILE
514
n
19
ILE
514
A
PRO
515
n
20
PRO
515
A
ASP
516
n
21
ASP
516
A
ALA
517
n
22
ALA
517
A
ASP
518
n
23
ASP
518
A
TYR
519
n
24
TYR
519
A
THR
520
n
25
THR
520
A
TRP
521
n
26
TRP
521
A
TYR
522
n
27
TYR
522
A
THR
523
n
28
THR
523
A
ASP
524
n
29
ASP
524
A
GLY
525
n
30
GLY
525
A
SER
526
n
31
SER
526
A
SER
527
n
32
SER
527
A
PHE
528
n
33
PHE
528
A
LEU
529
n
34
LEU
529
A
GLN
530
n
35
GLN
530
A
GLU
531
n
36
GLU
531
A
GLY
532
n
37
GLY
532
A
GLN
533
n
38
GLN
533
A
ARG
534
n
39
ARG
534
A
ARG
535
n
40
ARG
535
A
ALA
536
n
41
ALA
536
A
GLY
537
n
42
GLY
537
A
ALA
538
n
43
ALA
538
A
ALA
539
n
44
ALA
539
A
VAL
540
n
45
VAL
540
A
THR
541
n
46
THR
541
A
THR
542
n
47
THR
542
A
GLU
543
n
48
GLU
543
A
THR
544
n
49
THR
544
A
GLU
545
n
50
GLU
545
A
VAL
546
n
51
VAL
546
A
ILE
547
n
52
ILE
547
A
TRP
548
n
53
TRP
548
A
ALA
549
n
54
ALA
549
A
ARG
550
n
55
ARG
550
A
ALA
551
n
56
ALA
551
A
LEU
552
n
57
LEU
552
A
PRO
553
n
58
PRO
553
A
ALA
554
n
59
ALA
554
A
GLY
555
n
60
GLY
555
A
THR
556
n
61
THR
556
A
SER
557
n
62
SER
557
A
ALA
558
n
63
ALA
558
A
GLN
559
n
64
GLN
559
A
ARG
560
n
65
ARG
560
A
ALA
561
n
66
ALA
561
A
GLU
562
n
67
GLU
562
A
LEU
563
n
68
LEU
563
A
ILE
564
n
69
ILE
564
A
ALA
565
n
70
ALA
565
A
LEU
566
n
71
LEU
566
A
THR
567
n
72
THR
567
A
GLN
568
n
73
GLN
568
A
ALA
569
n
74
ALA
569
A
LEU
570
n
75
LEU
570
A
LYS
571
n
76
LYS
571
A
MET
572
n
77
MET
572
A
ALA
573
n
78
ALA
573
A
GLU
574
n
79
GLU
574
A
GLY
575
n
80
GLY
575
A
LYS
576
n
81
LYS
576
A
LYS
577
n
82
LYS
577
A
LEU
578
n
83
LEU
578
A
ASN
579
n
84
ASN
579
A
VAL
580
n
85
VAL
580
A
TYR
581
n
86
TYR
581
A
THR
582
n
87
THR
582
A
ASP
583
n
88
ASP
583
A
SER
584
n
89
SER
584
A
ARG
585
n
90
ARG
585
A
TYR
586
n
91
TYR
586
A
ALA
587
n
92
ALA
587
A
PHE
588
n
93
PHE
588
A
ALA
589
n
94
ALA
589
A
THR
590
n
95
THR
590
A
ALA
591
n
96
ALA
591
A
HIS
592
n
97
HIS
592
A
VAL
593
n
98
VAL
593
A
HIS
594
n
99
HIS
594
A
SER
606
n
100
SER
606
A
GLU
607
n
101
GLU
607
A
GLY
608
n
102
GLY
608
A
ARG
609
n
103
ARG
609
A
GLU
610
n
104
GLU
610
A
ILE
611
n
105
ILE
611
A
LYS
612
n
106
LYS
612
A
ASN
613
n
107
ASN
613
A
LYS
614
n
108
LYS
614
A
ASN
615
n
109
ASN
615
A
GLU
616
n
110
GLU
616
A
ILE
617
n
111
ILE
617
A
LEU
618
n
112
LEU
618
A
ALA
619
n
113
ALA
619
A
LEU
620
n
114
LEU
620
A
LEU
621
n
115
LEU
621
A
LYS
622
n
116
LYS
622
A
ALA
623
n
117
ALA
623
A
LEU
624
n
118
LEU
624
A
PHE
625
n
119
PHE
625
A
LEU
626
n
120
LEU
626
A
PRO
627
n
121
PRO
627
A
LYS
628
n
122
LYS
628
A
ARG
629
n
123
ARG
629
A
LEU
630
n
124
LEU
630
A
SER
631
n
125
SER
631
A
ILE
632
n
126
ILE
632
A
ILE
633
n
127
ILE
633
A
HIS
634
n
128
HIS
634
A
CYS
635
n
129
CYS
635
A
PRO
636
n
130
PRO
636
A
GLY
637
n
131
GLY
637
A
HIS
638
n
132
HIS
638
A
GLN
639
n
133
GLN
639
A
LYS
640
n
134
LYS
640
A
GLY
641
n
135
GLY
641
A
ASN
642
n
136
ASN
642
A
SER
643
n
137
SER
643
A
ALA
644
n
138
ALA
644
A
GLU
645
n
139
GLU
645
A
ALA
646
n
140
ALA
646
A
ARG
647
n
141
ARG
647
A
GLY
648
n
142
GLY
648
A
ASN
649
n
143
ASN
649
A
ARG
650
n
144
ARG
650
A
MET
651
n
145
MET
651
A
ALA
652
n
146
ALA
652
A
ASP
653
n
147
ASP
653
A
GLN
654
n
148
GLN
654
A
ALA
655
n
149
ALA
655
A
ALA
656
n
150
ALA
656
A
ARG
657
n
151
ARG
657
A
GLU
658
n
152
GLU
658
A
ALA
659
n
153
ALA
659
A
ALA
660
n
154
ALA
660
A
MET
661
n
155
MET
661
A
LYS
662
n
156
LYS
662
A
ALA
663
n
157
ALA
663
A
VAL
664
n
158
VAL
664
A
LEU
665
n
159
LEU
665
A
GLU
666
n
160
GLU
666
A
THR
667
n
161
THR
667
A
n
162
668
A
n
163
669
A
n
164
670
A
n
165
671
A
author_and_software_defined_assembly
PISA
1
monomeric
A
HOH
34
C
O
HOH
1_555
A
MG
163
B
MG
MG
1_555
A
HOH
115
C
O
HOH
1_555
170.7
A
HOH
34
C
O
HOH
1_555
A
MG
163
B
MG
MG
1_555
A
ASP
524
A
OD1
ASP
29
1_555
91.4
A
HOH
115
C
O
HOH
1_555
A
MG
163
B
MG
MG
1_555
A
ASP
524
A
OD1
ASP
29
1_555
81.7
A
HOH
34
C
O
HOH
1_555
A
MG
163
B
MG
MG
1_555
A
GLU
562
A
A
OE2
GLU
67
1_555
95.3
A
HOH
115
C
O
HOH
1_555
A
MG
163
B
MG
MG
1_555
A
GLU
562
A
A
OE2
GLU
67
1_555
90.9
A
ASP
524
A
OD1
ASP
29
1_555
A
MG
163
B
MG
MG
1_555
A
GLU
562
A
A
OE2
GLU
67
1_555
89.5
A
HOH
34
C
O
HOH
1_555
A
MG
163
B
MG
MG
1_555
A
ASP
583
A
OD1
ASP
88
1_555
84.5
A
HOH
115
C
O
HOH
1_555
A
MG
163
B
MG
MG
1_555
A
ASP
583
A
OD1
ASP
88
1_555
98.1
A
ASP
524
A
OD1
ASP
29
1_555
A
MG
163
B
MG
MG
1_555
A
ASP
583
A
OD1
ASP
88
1_555
148.9
A
GLU
562
A
A
OE2
GLU
67
1_555
A
MG
163
B
MG
MG
1_555
A
ASP
583
A
OD1
ASP
88
1_555
121.5
A
HOH
34
C
O
HOH
1_555
A
MG
163
B
MG
MG
1_555
A
ASP
583
A
OD2
ASP
88
1_555
71.5
A
HOH
115
C
O
HOH
1_555
A
MG
163
B
MG
MG
1_555
A
ASP
583
A
OD2
ASP
88
1_555
103.2
A
ASP
524
A
OD1
ASP
29
1_555
A
MG
163
B
MG
MG
1_555
A
ASP
583
A
OD2
ASP
88
1_555
98.8
A
GLU
562
A
A
OE2
GLU
67
1_555
A
MG
163
B
MG
MG
1_555
A
ASP
583
A
OD2
ASP
88
1_555
164.4
A
ASP
583
A
OD1
ASP
88
1_555
A
MG
163
B
MG
MG
1_555
A
ASP
583
A
OD2
ASP
88
1_555
50.7
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
A
O
LEU
552
A
O
LEU
57
A
N
ALA
536
A
N
ALA
41
A
O
ARG
535
A
O
ARG
40
A
N
PHE
528
A
N
PHE
33
A
N
THR
523
A
N
THR
28
A
O
TYR
581
A
O
TYR
86
A
N
VAL
580
A
N
VAL
85
A
O
ILE
633
A
O
ILE
127
1
A
GLY
496
A
GLY
1
1
Y
1
A
SER
497
A
SER
2
1
Y
1
A
ILE
498
A
ILE
3
1
Y
1
A
LEU
499
A
LEU
4
1
Y
1
A
SER
668
A
SER
162
1
Y
1
A
THR
669
A
THR
163
1
Y
1
A
LEU
670
A
LEU
164
1
Y
1
A
LEU
671
A
LEU
165
1
Y
1
A
GLU
666
85.39
-7.62
28.24
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.182
0.161
0.163
1.50
37.53
1122
21970
5.110
98.8
1.000
0.380
0.150
1
MOLECULAR REPLACEMENT
19.380
ML
FLAT BULK SOLVENT MODEL
60.00
0.40
1.50
37.53
162
1369
1
0
1206
0.006
1301
0.995
1778
12.100
505
0.064
200
0.004
236
0.2481
0.2145
1.5684
147
2497
95.00
0.2128
0.1783
1.6511
145
2611
99.00
0.2932
0.2048
1.7545
126
2587
99.00
0.2302
0.1853
1.8900
148
2593
99.00
0.1943
0.1569
2.0802
124
2648
99.00
0.1807
0.1551
2.3811
156
2612
100.00
0.1907
0.1584
2.9998
134
2637
100.00
0.1531
0.1526
37.5417
142
2663
100.00
1.500
37.530
3P1G
22272
0.098
1
7.800
6.770
99.900
0.771
1.500
1.550
2.1
1
3.660
99.300
0.750
1.550
1.620
2.4
1
5.090
100.000
0.665
1.620
1.690
3.0
1
7.110
100.000
0.318
1.690
1.780
3.6
1
7.410
100.000
0.266
1.780
1.890
4.3
1
7.420
100.000
0.236
1.890
2.040
5.9
1
7.270
100.000
0.178
2.040
2.240
7.2
1
7.270
100.000
0.144
2.240
2.560
8.5
1
7.460
100.000
0.095
2.560
3.230
11.8
1
7.570
100.000
0.050
3.230
37.530
24.2
1
7.360
99.800
data scaling
Jim W. Pflugrath
Jim.Pflugrath@Rigaku.com
Jul 17 2007
http://www.rigaku.com/software/dtrek.html
d*TREK
package
9.7L
phasing
Randy J. Read
cimr-phaser@lists.cam.ac.uk
http://www-structmed.cimr.cam.ac.uk/phaser/
PHASER
program
refinement
Paul D. Adams
PDAdams@lbl.gov
C++
http://www.phenix-online.org/
PHENIX
package
1.6.4_486
data extraction
PDB
deposit@deposit.rcsb.org
June 10, 2010
C++
http://sw-tools.pdb.org/apps/PDB_EXTRACT/
PDB_EXTRACT
package
3.10
Crystal Structure of the Xenotropic Murine Leukemia Virus-Related Virus (XMRV) RNase H Domain
1
N
N
2
N
N
3
N
N
A
SER
557
A
SER
62
HELX_P
A
ALA
573
A
ALA
78
1
1
17
A
SER
584
A
SER
89
HELX_P
A
VAL
593
A
VAL
98
1
2
10
A
ASN
613
A
ASN
107
HELX_P
A
LEU
624
A
LEU
118
1
3
12
A
SER
643
A
SER
137
HELX_P
A
LEU
665
A
LEU
159
1
4
23
metalc
2.589
A
HOH
34
C
O
HOH
1_555
A
MG
163
B
MG
MG
1_555
metalc
2.547
A
HOH
115
C
O
HOH
1_555
A
MG
163
B
MG
MG
1_555
metalc
2.341
A
MG
163
B
MG
MG
1_555
A
ASP
524
A
OD1
ASP
29
1_555
metalc
2.297
A
A
MG
163
B
MG
MG
1_555
A
GLU
562
A
OE2
GLU
67
1_555
metalc
2.355
A
MG
163
B
MG
MG
1_555
A
ASP
583
A
OD1
ASP
88
1_555
metalc
2.739
A
MG
163
B
MG
MG
1_555
A
ASP
583
A
OD2
ASP
88
1_555
TRANSCRIPTION
XMRV, RNase H, Reverse Transcriptase, TRANSCRIPTION
D0UFA6_9GAMR
UNP
1
1155
D0UFA6
ILAETHGTRPDLTDQPIPDADYTWYTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMAEGKK
LNVYTDSRYAFATAHVHGEIYRRRGLLTSEGREIKNKNEILALLKALFLPKRLSIIHCPGHQKGNSAEARGNRMADQAAR
EAAMKAVLETSTLL
1155
1328
3P1G
498
671
D0UFA6
A
1
3
165
1
expression tag
GLY
496
3P1G
A
D0UFA6
UNP
1
1
expression tag
SER
497
3P1G
A
D0UFA6
UNP
2
1
GLY
deletion
3P1G
A
D0UFA6
UNP
1252
1
GLU
deletion
3P1G
A
D0UFA6
UNP
1253
1
ILE
deletion
3P1G
A
D0UFA6
UNP
1254
1
TYR
deletion
3P1G
A
D0UFA6
UNP
1255
1
ARG
deletion
3P1G
A
D0UFA6
UNP
1256
1
ARG
deletion
3P1G
A
D0UFA6
UNP
1257
1
ARG
deletion
3P1G
A
D0UFA6
UNP
1258
1
GLY
deletion
3P1G
A
D0UFA6
UNP
1259
1
LEU
deletion
3P1G
A
D0UFA6
UNP
1260
1
LEU
deletion
3P1G
A
D0UFA6
UNP
1261
1
THR
deletion
3P1G
A
D0UFA6
UNP
1262
5
anti-parallel
anti-parallel
parallel
parallel
A
VAL
546
A
VAL
51
A
LEU
552
A
LEU
57
A
GLN
533
A
GLN
38
A
THR
541
A
THR
46
A
TYR
519
A
TYR
24
A
GLN
530
A
GLN
35
A
LYS
577
A
LYS
82
A
THR
582
A
THR
87
A
ARG
629
A
ARG
123
A
HIS
634
A
HIS
128
BINDING SITE FOR RESIDUE MG A 163
A
MG
163
Software
5
A
HOH
34
C
HOH
5
1_555
A
HOH
115
C
HOH
5
1_555
A
ASP
524
A
ASP
29
5
1_555
A
GLU
562
A
GLU
67
5
1_555
A
ASP
583
A
ASP
88
5
1_555
76
P 41